Phenotype Curation

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Phenotype Annotation

Annotate phenotypes to strains. Strain curation can be difficult becasue of incomplete information in the publication. Learn a minimum from the paper or by asking authors to create a strain where the phenotype(s) then can be associated.




Dicty Phenotype Ontology

The Dicty Phenotype Ontology is a hierarchical controlled vocabulary used for annotating strains with phenotypes.
  • Terms from the Dicty Phenotype Ontology must be used for phenotype annotations.
  • If you require a phenotype term not present in the phenotype ontology, make a request in the Issue Tracker, marking the section 'Phenotype Ontology.'
  • After all curators approve the changes, follow the instructions for editing the Ontology.




Dicty Assay

The Dicty Assay list is a controlled vocabulary to describe the experiment used to obtain the phenotype.
  • Terms from the Dicty Assay list contain nuclei count and uptake of latex beads.
  • The list is currently small and needs expansion.
  • The list is stored as an .obo file and needs to be updated like any other ontology.




Environmental Condition

The Environmental Condition list is a controlled vocabulary to describe the conditions under which the experiment has been done to obtain the phenotype.
  • Terms from the Dicty Assay contain at low cell density, uptake of latex beads, and on bacterial plates.
  • The list is currently small and needs expansion.
  • The list is stored as an .obo file and needs to be updated like any other ontology.




Notes

The Notes field is a free text field where any information should be entered that cannot be captured otherwise.
  • Examples:
    • defect milder than in silenced enlA cells
    • rescues the cytokinesis defect of ctxA- mutants
  • If several strains are reported in the paper and it is not clear which one is shown in the experiment, choose the most likely strain and add all phenotypes. Then add the dominant phenotype to the other strains and add a note with a link to the phenotype details of the fully annotated strain. See this Phenotype and Strain Details Page.




Editing the Dicty Ontologies

The following workflow should be used to edit the ontologies to ensure proper versioning and integration into the database
  • In CVS on your own machine, 'Update' your ontology to the most current version.
  • Edit the ontology on your own machine using OBO-Edit (when loading, make sure you use the file path to the obo file on your own machine). Add dbxref DDB:yourinitials when editing. Commit changes in OBO-Edit.
  • 'Save As' on your own machine (make sure file path is correct).
  • In CVS on your own machine, commit the edited file.
  • 'Update' the ontology on cgm-1 with CVS.
  • Click on 'Update Dicty Phenotype and Mutant Types Ontology' on testdb. Wait a few moments and the ontologies will be loaded.
  • Check testdb to see that your changes have been made.
  • 'Update' the ontology on cgm-2 with CVS.
  • Click on 'Update Dicty Phenotype and Mutant Types Ontology' on production. Wait a few moments and the ontologies will be loaded.
  • Check production to see that your changes have been made.


Annotation Guidelines

No known phenotype

When both 'no known phenotype' and a mutant phenotype annotations exist for a gene
  • If the annotations are derived from the same publication, omit 'no known phenotype' and annotate only the mutant phenotype.
  • If the annotations come from different publications, keep 'no known phenotype' and qualify it with conditional information. See for example canA.




Multiple developmental phenotypes

Similar developmental phenotypes are allowed. For example, if authors show small aggregation territory AND small fruiting bodies, annotate to both phenotype terms. Not all small aggregates produce small fruiting bodies, and conversely, not all small fruiting bodies arise from small aggregation territories. Annotate to both phenotype terms if authors show both.





Phenotype Resources



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